MoleculeSet.java

/* $RCSfile$ * $Author$ * $Date$ * $Revision$ * * Copyright (C) 1997-2007 Christoph Steinbeck <steinbeck@users.sf.net> * * Contact: cdk-devel@lists.sourceforge.net * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */package org.openscience.cdk;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
/** * A set of molecules, for example those taking part in a reaction. * * To retrieve the molecules from the set, there are two options: * * <pre> * Molecule[] mols = setOfMolecules.getMolecules(); * for (int i=0; i < mols.length; i++) { * Molecule mol = mols[i]; * } * </pre> * * and * * <pre> * for (int i=0; i < setOfMolecules.getMoleculeCount(); i++) { * Molecule mol = setOfMolecules.getMolecule(i); * } * </pre> * * @cdk.module data * @cdk.githash * * @cdk.keyword reaction * @cdk.keyword molecule */00057publicclass MoleculeSetextendsAtomContainerSet implements IMoleculeSet, Cloneable {
/** * Determines if a de-serialized object is compatible with this class. * * This value must only be changed if and only if the new version * of this class is incompatible with the old version. See Sun docs * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide * /serialization/spec/version.doc.html>details</a>. * */00068privatestaticfinallongserialVersionUID = -861287315770869699L;
publicMoleculeSet() {}
/** * Adds an atomContainer to this container. * * @param atomContainer The IMolecule to be added to this container * @throws IllegalArgumentException when the passed IAtomContainer is not * an IMolecule. */00079publicvoidaddAtomContainer(IAtomContainer atomContainer) {
if (!(atomContainer instanceof IMolecule))
thrownew IllegalArgumentException(
"Only IMolecule's can be stored in an IMoleculeSet"
);
super.addAtomContainer(atomContainer);
}
/** * Adds an atomContainer to this container with the given * multiplier. * * @param atomContainer The atomContainer to be added to this container * @param multiplier The multiplier of this atomContainer * @throws IllegalArgumentException when the passed IAtomContainer is not * an IMolecule. */00096publicvoidaddAtomContainer(IAtomContainer atomContainer, double multiplier) {
if (!(atomContainer instanceof IMolecule))
thrownew IllegalArgumentException(
"Only IMolecule's can be stored in an IMoleculeSet"
);
super.addAtomContainer(atomContainer, multiplier);
}
/** * Adds an molecule to this container. * * @param molecule The molecule to be added to this container */00109publicvoidaddMolecule(IMolecule molecule) {
super.addAtomContainer(molecule);
/* notifyChanged() called in super.addAtomContainer() */
}
/** * Adds all molecules in the MoleculeSet to this container. * * @param moleculeSet The MoleculeSet */00119publicvoidadd(IMoleculeSet moleculeSet) {
for (IAtomContainer mol : moleculeSet.molecules()) {
addAtomContainer(mol);
}
}
00125publicvoidsetMolecules(IMolecule[] molecules)
{
if (atomContainerCount > 0) removeAllAtomContainers();
for (IMolecule molecule : molecules) {
addMolecule(molecule);
}
}
/** * Returns the array of Molecules of this container. * * @return The array of Molecules of this container * @see #setMolecules */00139public Iterable<IAtomContainer> molecules() {
return super.atomContainers();
}
/** * * Returns the Molecule at position <code>number</code> in the * container. * * @param number The position of the Molecule to be returned. * @return The Molecule at position <code>number</code> . */00152publicIMoleculegetMolecule(int number)
{
return (IMolecule)super.getAtomContainer(number);
}
/** * Returns the number of Molecules in this Container. * * @return The number of Molecules in this Container */00163publicintgetMoleculeCount() {
return super.getAtomContainerCount();
}
/** * Clones this MoleculeSet and its content. * *@return the cloned object */00173public Object clone() throws CloneNotSupportedException {
return (MoleculeSet)super.clone();
}
00177public String toString() {
StringBuffer buffer = new StringBuffer();
buffer.append("MoleculeSet(");
buffer.append(super.toString());
buffer.append(')');
return buffer.toString();
}
/** * Called by objects to which this object has * registered as a listener. * *@param event A change event pointing to the source of the change */00191publicvoidstateChanged(IChemObjectChangeEvent event)
{
notifyChanged(event);
}
}